I've been pondering this since you posted, and thought I'd make a couple observations just because.

Please note, I am not a doctor, nor to I play one on TV, and I didn't stay in a Holiday Inn Express last night. I have no training in biology/biochemistry beyond basic High School biology and what just about anyone can gain thru internet searches.

That said.....

Comparing the 8,000 species of bacteria in the gut of an indigenous person to the 250 in someone living in "modern" conditions: How many of those lost species are truly beneficial, how many are a response to a pressure that's not present in modern life, and how many are at best mildly parasitical? I don't know if this is caused by a bacteria, but I recall reading that the sickle cell played a role in preventing malaria, trading something that MAY kill you years down the road to protect against something that may kill you NOW. Life is always a trade-off.

While I'm certainly not a fan of anti-bacterial everything, and I'm a firm believer that killing off all the germs in our environment is what brings about an increase in allergies (the immune system responding to something that's not a threat because it's never had a chance to respond to something that IS), lots of people are alive today because of antibiotics and vaccines. My mother had a cousin who died of tetanus (she called it lockjaw) after burning himself with a cap gun (which is why cap guns were verboten in the D household growing up). Today that wouldn't even be an issue, a quick shot in the arm at the ER, or just a booster as part of a routine check-up. How often did people (even healthy people) die of the flu before antibiotics? Now only the people who are already compromised in some manner do so. While a more targeted approach would probably be even better, if given the choice between dying of infection in the next few days, or surviving then having to deal with rebuilding my intestinal environment, well option 2 sounds pretty good.

(Just as an aside, note that most of the diseases that are BIG killers don't naturally use humans as hosts, they've jumped species. Killing your host, especially quickly, isn't a good choice for a disease that wants to be passed on, note how quickly Ebola tends to burn out when it hits an area in Africa. IIRC rodents can carry Plague for years, but it kills humans quickly.)

How much of the increase in diseases like cancer is simply because we live longer? Diseases that kill you after your children are grown are genetically irrelevant. I recall being told once that if he lives long enough, a man will either die OF prostate cancer or WITH it. Add 20 years to the average life expectancy in a century and all sorts of things become issues that never were before, things like cancer and alzhiemers. Plus, significant numbers of people now survive cancer when they're younger and reproduce, for cancers with a genetic component, those genes are passed on.

Mind you, I'm not saying your wrong in looking at the human body as an ecosystem instead of a machine, nor am I saying that our view of diseases (of all sorts) doesn't need to change. I'm just noting that within my lifetime I've seen it go from 90 being an extremely old person spending their days in a chair in an "old people's home" to having a mother-in-law who's 88 and still plays tennis.

Those 8,000 species are not believed to be pathogenic. They are thought to be of the same nature as the indigenous ones, which cannot be cultured - pretty much, by definition, a pathogen would be able to be cultured.

The situation with food allergies is becoming quite serious - and there appears to be a link between digestive flora and obesity.

Provided they aren't done irresponsibly, vaccines are up there with hygiene as a benefit of modern life

I know antibiotics have saved lives - but they aren't a panacea, and, frankly, they are rapidly losing any effectiveness.

In theory, a bacteriophage based therapy would work - and has worked well on MSRA - and bacteria couldn't become resistant to it.

But, getting the FDA onboard would take an act of Congress, and some serious brow-beating, and someone in that area of research - which was a tiny handful of folks - may have increased some with the new interest in intestinal flora - to start talking to politicians.

? Totally different scenario/mechanism. Bacteriophage therapy, more or less, is based on amplifying the bacteriophage already present/normally present, to control an overgrowth of bacteria - its about restoring environmental balance to the biome, rather than clear cutting it.

(It has to be done carefully, and has been, thus far. Some "surprises" have been found (probably the "plague of sores.), but seems to have good results.)